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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ), 'gf_id' => 'HOM05D001147', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001147' ), 'data_identifier' => 'HOM05D001147', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001147', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p07340' => 'bna', 'A02p08160' => 'bna', 'A03p12540' => 'bna', 'A03p12560' => 'bna', 'A04p05080' => 'bna', 'A05p37500' => 'bna', 'A06p14280' => 'bna', 'A09p47670' => 'bna', 'A09p56540' => 'bna', 'A10p15210' => 'bna', 'A10p29840' => 'bna', 'Aa31LG2G19550' => 'aar', 'Aa31LG3G10630' => 'aar', 'Aa31LG3G13670' => 'aar', 'Aa31LG3G5710' => 'aar', 'Aa31sc167G40' => 'aar', 'Aa31sc32G60' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4650' => 'aag', 'Actinidia03853' => 'ach', 'Actinidia26812' => 'ach', 'Actinidia37780' => 'ach', 'Actinidia38663' => 'ach', 'Ah.01g007320' => 'amhyb', 'Ah.02g116060' => 'amhyb', 'Ah.09g228730' => 'amhyb', 'Ah.11g041790' => 'amhyb', 'AL1G30640' => 'aly', 'AL3G23420' => 'aly', 'AL4G14260' => 'aly', 'AL5G35810' => 'aly', 'AL6G16650' => 'aly', 'AL7G21290' => 'aly', 'AL8G33880' => 'aly', 'Aqoxy1G00579' => 'aox', 'Aqoxy6G00670' => 'aox', 'Aqoxy7G02387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6KF5RS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7IC8PF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9WK6R8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQXN30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS6RY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DTZ5L4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GV0XVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6YE5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IW6P38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PH0WUV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RXWW1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TE56A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U2WZ8A' => 'arhy', 'AT1G18265' => 'ath', 'AT2G24140' => 'ath', 'AT3G11850' => 'ath', 'AT3G54740' => 'ath', 'AT4G30830' => 'ath', 'AT5G06560' => 'ath', 'AT5G57830' => 'ath', 'ATR0697G064' => 'atr', 'ATR0739G021' => 'atr', 'ATR0767G260' => 'atr', 'Atru.chr6.1317' => 'acertr', 'Atru.chr7.337' => 'acertr', 'Atru.chr7.338' => 'acertr', 'Atru.chr8.1278' => 'acertr', 'AUR62010738' => 'cqu', 'AUR62025358' => 'cqu', 'AUR62028359' => 'cqu', 'AUR62036306' => 'cqu', 'AUR62038415' => 'cqu', 'AUR62044712' => 'cqu', 'AUR62044713' => 'cqu', 'BcaB01g00164' => 'bca', 'BcaB01g03245' => 'bca', 'BcaB02g07725' => 'bca', 'BcaB02g08457' => 'bca', 'BcaB04g21112' => 'bca', 'BcaB05g21662' => 'bca', 'BcaB05g21663' => 'bca', 'BcaB05g22378' => 'bca', 'BcaB05g23326' => 'bca', 'BcaB06g25569' => 'bca', 'BcaB06g25570' => 'bca', 'BcaB06g26547' => 'bca', 'BcaB07g31815' => 'bca', 'BcaB07g32740' => 'bca', 'BcaB08g36150' => 'bca', 'BcaC02g09700' => 'bca', 'BcaC04g19923' => 'bca', 'BcaC05g25720' => 'bca', 'BcaC05g28240' => 'bca', 'BcaC05g28241' => 'bca', 'BcaC05g29317' => 'bca', 'BcaC07g39790' => 'bca', 'BcaC07g40956' => 'bca', 'BcaC08g44694' => 'bca', 'BcaC09g48190' => 'bca', 'BcaC09g51873' => 'bca', 'BcaNung02737' => 'bca', 'BcaNung03435' => 'bca', 'BcaNung03762' => 'bca', 'BcaNung06693' => 'bca', 'BcaNung06847' => 'bca', 'BolC1t00797H' => 'bol', 'BolC1t05285H' => 'bol', 'BolC2t06240H' => 'bol', 'BolC2t07500H' => 'bol', 'BolC3t13916H' => 'bol', 'BolC4t25324H' => 'bol', 'BolC5t30351H' => 'bol', 'BolC5t33009H' => 'bol', 'BolC5t34273H' => 'bol', 'BolC6t37416H' => 'bol', 'BolC8t50599H' => 'bol', 'BolC8t51522H' => 'bol', 'BolC9t57824H' => 'bol', 'BolC9t59765H' => 'bol', 'BraA01t00682Z' => 'bra', 'BraA01t04156Z' => 'bra', 'BraA02t04883Z' => 'bra', 'BraA02t05890Z' => 'bra', 'BraA03t10570Z' => 'bra', 'BraA03t10571Z' => 'bra', 'BraA03t15076Z' => 'bra', 'BraA04t16219Z' => 'bra', 'BraA05t22548Z' => 'bra', 'BraA06t24557Z' => 'bra', 'BraA09t40223Z' => 'bra', 'BraA09t41044Z' => 'bra', 'BraA10t43604Z' => 'bra', 'BraA10t45022Z' => 'bra', 'C01p08090' => 'bna', 'C02p02750' => 'bna', 'C02p13810' => 'bna', 'C03p14740' => 'bna', 'C04p37580' => 'bna', 'C05p16540' => 'bna', 'C05p42810' => 'bna', 'C05p56060' => 'bna', 'C06p22300' => 'bna', 'C08p29880' => 'bna', 'C08p39480' => 'bna', 'C09p49730' => 'bna', 'C09p70210' => 'bna', 'CAN.G128.167' => 'can', 'CAN.G13221.1' => 'can', 'CAN.G160.1' => 'can', 'CAN.G409.2' => 'can', 'CAN.G504.77' => 'can', 'CAN.G551.65' => 'can', 'CAN.G56.21' => 'can', 'CAN.G606.1' => 'can', 'CAN.G782.28' => 'can', 'CANSAT11G0976' => 'cansat', 'CANSAT54G2207' => 'cansat', 'CANSAT64G1996' => 'cansat', 'CARHR018820' => 'chi', 'CARHR086410' => 'chi', 'CARHR118150' => 'chi', 'CARHR164680' => 'chi', 'CARHR206640' => 'chi', 'CARHR238680' => 'chi', 'CARHR271570' => 'chi', 'Carub.0001s1788' => 'cru', 'Carub.0003s1120' => 'cru', 'Carub.0004s0332' => 'cru', 'Carub.0005s2134' => 'cru', 'Carub.0006s0544' => 'cru', 'Carub.0007s0973' => 'cru', 'Carub.0008s1836' => 'cru', 'Ca_03163_v3' => 'car', 'Ca_09084_v3' => 'car', 'Ca_11650_v3' => 'car', 'Ca_18403_v3' => 'car', 'Ca_21150_v3' => 'car', 'CBR_g12419' => 'cbr', 'Cc02_g20730' => 'ccan', 'Cc06_g07000' => 'ccan', 'Cc06_g14570' => 'ccan', 'CDE01G0500' => 'cde', 'CDE02G4658' => 'cde', 'CDE04G0308' => 'cde', 'CDE04G2413' => 'cde', 'CDE05G0928' => 'cde', 'CDE05G2083' => 'cde', 'CDE05G2853' => 'cde', 'CDE06G0305' => 'cde', 'CDE07G0737' => 'cde', 'CDE07G1344' => 'cde', 'Cfa004825' => 'cfa', 'Cfa004826' => 'cfa', 'Cfa020794' => 'cfa', 'Ciclev10010396m.g' => 'ccl', 'Ciclev10011510m.g' => 'ccl', 'CiPaw.06G159200' => 'cil', 'CiPaw.09G024400' => 'cil', 'CiPaw.10G021600' => 'cil', 'CiPaw.16G107300' => 'cil', 'ClCG06G012580' => 'cla', 'ClCG10G009680' => 'cla', 'ClCG10G017930' => 'cla', 'COL.COLO4_23938' => 'col', 'COL.COLO4_29482' => 'col', 'COL.COLO4_32417' => 'col', 'Cpa.g.sc20.30' => 'cpa', 'Cpa.g.sc222.10' => 'cpa', 'Cpa.g.sc46.192' => 'cpa', 'CsaV3_3G038360' => 'csa', 'CSS0001493' => 'camsi', 'CSS0011357' => 'camsi', 'CSS0032070' => 'camsi', 'CSS0049954' => 'camsi', 'DCAR_009076' => 'dca', 'DCAR_013463' => 'dca', 'DCAR_014802' => 'dca', 'DCAR_016905' => 'dca', 'DCAR_019416' => 'dca', 'DCAR_020677' => 'dca', 'DCAR_021900' => 'dca', 'Dinv11902' => 'din', 'Dinv25082' => 'din', 'Dinv41347' => 'din', 'Dinv42826' => 'din', 'Dinv43274' => 'din', 'Duzib093G1464' => 'dzi', 'Duzib106G0463' => 'dzi', 'Duzib128G1747' => 'dzi', 'Duzib132G0186' => 'dzi', 'Duzib187G1988' => 'dzi', 'ECA234G2491' => 'eca', 'ECA236G3004' => 'eca', 'ECA238G2006' => 'eca', 'ECA248G2244' => 'eca', 'EL10Ac5g10891' => 'bvu', 'EL10Ac5g11802' => 'bvu', 'EL10Ac8g18921' => 'bvu', 'Eucgr.A02540' => 'egr', 'Eucgr.C02510' => 'egr', 'Eucgr.K01910' => 'egr', 'FAN02G0555' => 'fan', 'FAN02G2541' => 'fan', 'FAN02G3484' => 'fan', 'FAN02G3619' => 'fan', 'FAN05G1203' => 'fan', 'FAN05G3895' => 'fan', 'FAN14G3554' => 'fan', 'FAN23G2262' => 'fan', 'FAN26G2137' => 'fan', 'FAN28G1301' => 'fan', 'FvH4_1g00620' => 'fve', 'FvH4_6g21080' => 'fve', 'Glyma.02G166500' => 'gma', 'Glyma.02G206200' => 'gma', 'Glyma.03G205300' => 'gma', 'Glyma.04G155400' => 'gma', 'Glyma.08G066500' => 'gma', 'Glyma.09G087800' => 'gma', 'Glyma.10G087300' => 'gma', 'Glyma.15G194200' => 'gma', 'Glyma.17G071800' => 'gma', 'Glyma.19G202800' => 'gma', 'Gohir.A01G136100' => 'ghi', 'Gohir.A01G136150' => 'ghi', 'Gohir.A01G199400' => 'ghi', 'Gohir.A08G088200' => 'ghi', 'Gohir.A08G236000' => 'ghi', 'Gohir.A09G132000' => 'ghi', 'Gohir.A13G050000' => 'ghi', 'Gohir.D01G123200' => 'ghi', 'Gohir.D01G189500' => 'ghi', 'Gohir.D08G099300' => 'ghi', 'Gohir.D08G256400' => 'ghi', 'Gohir.D09G128300' => 'ghi', 'Gohir.D13G048800' => 'ghi', 'Gorai.002G154100' => 'gra', 'Gorai.002G233200' => 'gra', 'Gorai.004G107100' => 'gra', 'Gorai.004G273600' => 'gra', 'Gorai.006G146900' => 'gra', 'Gorai.013G054500' => 'gra', 'GSVIVG01022511001' => 'vvi', 'GSVIVG01023657001' => 'vvi', 'HanXRQChr01g0026211' => 'han', 'HanXRQChr02g0052841' => 'han', 'HanXRQChr05g0141651' => 'han', 'HanXRQChr10g0297711' => 'han', 'HanXRQChr11g0347701' => 'han', 'HanXRQChr12g0357791' => 'han', 'HanXRQChr14g0453211' => 'han', 'Haze_10471' => 'cav', 'Haze_19151' => 'cav', 'Haze_20132' => 'cav', 'Hma1.2p1_0127F.1_g059730' => 'hma', 'Hma1.2p1_0304F.1_g119330' => 'hma', 'HPP92_000980' => 'vpl', 'HPP92_011038' => 'vpl', 'HPP92_012151' => 'vpl', 'HPP92_013932' => 'vpl', 'HPP92_017666' => 'vpl', 'HPP92_020607' => 'vpl', 'HPP92_028939' => 'vpl', 'Hund07637' => 'sun', 'Hund10786' => 'sun', 'Hund15015' => 'sun', 'Lalb_Chr01g0017701' => 'lal', 'Lalb_Chr02g0154161' => 'lal', 'Lalb_Chr05g0217941' => 'lal', 'Lalb_Chr06g0173231' => 'lal', 'Lalb_Chr07g0179961' => 'lal', 'Lalb_Chr08g0234221' => 'lal', 'Lalb_Chr09g0326981' => 'lal', 'Lalb_Chr11g0072491' => 'lal', 'Lalb_Chr18g0060361' => 'lal', 'Lalb_Chr21g0316331' => 'lal', 'Lalb_Chr23g0275651' => 'lal', 'Lalb_Chr25g0287821' => 'lal', 'Lj1g0012618' => 'lja', 'Lj4g0005943' => 'lja', 'Lj4g0012991' => 'lja', 'Lj5g0015223' => 'lja', 'Lj6g0014397' => 'lja', 'Lj6g0023022' => 'lja', 'Lj7C138T2' => 'lonja', 'Lj9C346T12' => 'lonja', 'Lj9C720G1' => 'lonja', 'Lsat_1_v5_gn_1_56540' => 'lsa', 'Lsat_1_v5_gn_2_102020' => 'lsa', 'Lsat_1_v5_gn_5_110461' => 'lsa', 'Lsat_1_v5_gn_6_34261' => 'lsa', 'Lsat_1_v5_gn_8_64600' => 'lsa', 'Manes.06G031400' => 'mes', 'Manes.07G043300' => 'mes', 'Manes.08G037800' => 'mes', 'Manes.09G041600' => 'mes', 'Manes.10G095700' => 'mes', 'Manes.14G142200' => 'mes', 'Mapoly0056s0058' => 'mpo', 'MBI05_g41587_MAGBIO' => 'mbi', 'MBI11_g39497_MAGBIO' => 'mbi', 'MBI14_g08688_MAGBIO' => 'mbi', 'MD02G1005000' => 'mdo', 'MD10G1055500' => 'mdo', 'MD12G1046400' => 'mdo', 'MD14G1045000' => 'mdo', 'MD15G1149000' => 'mdo', 'Medtr1g054835' => 'mtr', 'Medtr4g093150' => 'mtr', 'Medtr4g130400' => 'mtr', 'Medtr7g107000' => 'mtr', 'MELO3C009579.2' => 'cme', 'MELO3C010205.2' => 'cme', 'Migut.B00533' => 'egut', 'Migut.J00727' => 'egut', 'Migut.J01385' => 'egut', 'Migut.L01839' => 'egut', 'MSTRG.10410' => 'ama', 'MSTRG.10712' => 'ama', 'MSTRG.16625' => 'ama', 'MSTRG.26260' => 'ama', 'MSTRG.26595' => 'ama', 'MSTRG.6159' => 'ama', 'Nitab4.5_0000117g0010' => 'nta', 'Nitab4.5_0000123g0100' => 'nta', 'Nitab4.5_0000300g0010' => 'nta', 'Nitab4.5_0000721g0020' => 'nta', 'Nitab4.5_0002131g0080' => 'nta', 'Nitab4.5_0002329g0210' => 'nta', 'Nitab4.5_0002750g0010' => 'nta', 'Nitab4.5_0003551g0080' => 'nta', 'Nitab4.5_0005908g0060' => 'nta', 'Nitab4.5_0007324g0050' => 'nta', 'Nitab4.5_0008310g0040' => 'nta', 'Nitab4.5_0011991g0010' => 'nta', 'Nitab4.5_0012842g0020' => 'nta', 'Nn2g14425' => 'nnu', 'Nn6g34580' => 'nnu', 'Nn8g40006' => 'nnu', 'Oeu020154.1' => 'oeu', 'Oeu021339.1' => 'oeu', 'Oeu035657.1' => 'oeu', 'Oeu045028.1' => 'oeu', 'Oeu059898.1' => 'oeu', 'Oeu063078.1' => 'oeu', 'Os03g0650800' => 'osa', 'Os03g0789200' => 'osa', 'Os07g0162200' => 'osa', 'Os08g0269000' => 'osa', 'Os08g0442350' => 'osa', 'Os11g0575900' => 'osa', 'Os12g0488700' => 'osa', 'Peaxi162Scf00003g05359' => 'pax', 'Peaxi162Scf00024g02614' => 'pax', 'Peaxi162Scf00062g00014' => 'pax', 'Peaxi162Scf00062g00015' => 'pax', 'Peaxi162Scf00062g00112' => 'pax', 'Peaxi162Scf00203g00028' => 'pax', 'Peaxi162Scf00210g00617' => 'pax', 'Peaxi162Scf00261g00055' => 'pax', 'Peaxi162Scf01313g00230' => 'pax', 'Peaxi162Scf01313g00232' => 'pax', 'PGR004G0917' => 'pgr', 'PGR102G2166' => 'pgr', 'PGR142G2639' => 'pgr', 'PGR142G3594' => 'pgr', 'PGSC0003DMG400007910' => 'stu', 'PGSC0003DMG400008664' => 'stu', 'PGSC0003DMG400009262' => 'stu', 'PGSC0003DMG400010672' => 'stu', 'PGSC0003DMG400011151' => 'stu', 'PGSC0003DMG400028131' => 'stu', 'Phvul.001G198800' => 'pvu', 'Phvul.003G154100' => 'pvu', 'Phvul.006G200900' => 'pvu', 'Phvul.007G265000' => 'pvu', 'Phvul.009G196200' => 'pvu', 'Potri.006G181300' => 'ptr', 'Potri.006G199000' => 'ptr', 'Potri.009G078800' => 'ptr', 'Potri.016G065200' => 'ptr', 'Potri.018G103500' => 'ptr', 'Prupe.7G090000' => 'ppe', 'Prupe.7G266000' => 'ppe', 'Prupe.8G073500' => 'ppe', 'Psat0s5104g0040' => 'psa', 'Psat1g025880' => 'psa', 'Psat3g027160' => 'psa', 'Psat7g006720' => 'psa', 'Psat7g101960' => 'psa', 'PSO339G2961' => 'pso', 'PSO339G5757' => 'pso', 'PSO384G2296' => 'pso', 'PSO384G2439' => 'pso', 'PSO541G3519' => 'pso', 'PSO675G5607' => 'pso', 'PSO782G1029' => 'pso', 'QL02p093985' => 'qlo', 'QL07p026225' => 'qlo', 'QL11p025923' => 'qlo', 'QL11p026401' => 'qlo', 'RcHm_v2.0_Chr2g0085241' => 'rch', 'RcHm_v2.0_Chr3g0477461' => 'rch', 'Rhsim03G0058400' => 'rsi', 'Rhsim05G0100200' => 'rsi', 'Sabra06G0138200' => 'sbr', 'Sabra06G0152900' => 'sbr', 'Sabra16G0066800' => 'sbr', 'SalBow1G2628' => 'sbo', 'SalBow1G4907' => 'sbo', 'SalBow1G7781' => 'sbo', 'SalBow1G8021' => 'sbo', 'SalBow6G4101' => 'sbo', 'SalBow6G4823' => 'sbo', 'Sc01g0005670' => 'sci', 'Sc07g0007270' => 'sci', 'Sc08g0004010' => 'sci', 'Sc18g0003070' => 'sci', 'Sed0005842' => 'sed', 'Sed0008388' => 'sed', 'Sed0017307' => 'sed', 'Sed0021973' => 'sed', 'Sed0026266' => 'sed', 'SEGI_23857' => 'sgi', 'SEGI_30536' => 'sgi', 'SEGI_31720' => 'sgi', 'SGA_v2.0_scaffold112G31565' => 'sas', 'SGA_v2.0_scaffold184G40035' => 'sas', 'SGA_v2.0_scaffold222G42784' => 'sas', 'SGA_v2.0_scaffold265G46086' => 'sas', 'SGA_v2.0_scaffold32G12939' => 'sas', 'SGA_v2.0_scaffold41G15768' => 'sas', 'Solyc01g106100.2' => 'sly', 'Solyc07g005910.3' => 'sly', 'Solyc10g081620.2' => 'sly', 'Solyc11g020850.3' => 'sly', 'Solyc11g045480.3' => 'sly', 'Solyc12g009900.3' => 'sly', 'Sopen01g048490' => 'spe', 'Sopen07g002040' => 'spe', 'Sopen10g032130' => 'spe', 'Sopen11g011020' => 'spe', 'Sopen11g021110' => 'spe', 'Sopen12g004780' => 'spe', 'Sp1g16230' => 'spa', 'Sp3g10080' => 'spa', 'Sp4g03090' => 'spa', 'Sp5g07710' => 'spa', 'Sp6g19520' => 'spa', 'Sp6g36300' => 'spa', 'Sp7g28710' => 'spa', 'TAR049G0007' => 'tar', 'TAR531G0003' => 'tar', 'TAR623G1361' => 'tar', 'TAR626G1737' => 'tar', 'TAR628G1061' => 'tar', 'TAR636G1242' => 'tar', 'THA.LOC104799264' => 'tha', 'THA.LOC104803557' => 'tha', 'THA.LOC104803906' => 'tha', 'THA.LOC104804423' => 'tha', 'THA.LOC104807189' => 'tha', 'THA.LOC104809943' => 'tha', 'THA.LOC104813537' => 'tha', 'THA.LOC104825241' => 'tha', 'Thecc.02G126800' => 'tca', 'Thecc.05G183700' => 'tca', 'Thecc.09G153000' => 'tca', 'Thhalv10000280m.g' => 'esa', 'Thhalv10008550m.g' => 'esa', 'Thhalv10010393m.g' => 'esa', 'Thhalv10013131m.g' => 'esa', 'Thhalv10013794m.g' => 'esa', 'Thhalv10020560m.g' => 'esa', 'Thhalv10025538m.g' => 'esa', 'TPR.G11221' => 'tpr', 'TPR.G14467' => 'tpr', 'TPR.G18496' => 'tpr', 'TPR.G24887' => 'tpr', 'TPR.G34439' => 'tpr', 'TWI34G0284' => 'twi', 'TWI53G1194' => 'twi', 'TWI74G1171' => 'twi', 'unitig_21.g20699' => 'ugi', 'unitig_22.g5994' => 'ugi', 'unitig_26.g9150' => 'ugi', 'unitig_37.g12749' => 'ugi', 'unitig_578.g16354' => 'ugi', 'unitig_744.g24194' => 'ugi', 'unitig_8.g4734' => 'ugi', 'vmacro06057' => 'vma', 'vmacro07514' => 'vma', 'VMungo0251G1196' => 'vmu', 'VMungo0720G2965' => 'vmu', 'VMungo1215G2388' => 'vmu', 'VMungo1309G1356' => 'vmu', 'VMungo1383G2824' => 'vmu', 'Zm00001eb041080' => 'zma', 'Zm00001eb052960' => 'zma', 'Zm00001eb060170' => 'zma', 'Zm00001eb114280' => 'zma', 'Zm00001eb213200' => 'zma', 'Zm00001eb218460' => 'zma', 'Zm00001eb408700' => 'zma', 'Zm00001eb412110' => 'zma' ) $gf_id = 'HOM05D001147' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001147' ) $data_identifier = 'HOM05D001147' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 24, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 31, 'bol' => (int) 14, 'bra' => (int) 14, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 12, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 13, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 7, 'pax' => (int) 10, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 6, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 7, 'tar' => (int) 6, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 5, 'twi' => (int) 3, 'ugi' => (int) 7, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412110' $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